"""!
Read/Write Serafin files and manipulate associated data.

Handles Serafin file with:
  - single and double precision
  - big and little endian

The sizes (file, header, frame) are in bytes (8 bits).
"""

import copy
import numpy as np
import os
from shapely.geometry import LinearRing
import struct

from pyteltools.conf import settings
from pyteltools.slf.variable.variables_2d import VARIABLES_2D
from pyteltools.slf.variable.variables_3d import VARIABLES_3D

from .util import logger


# Encoding Information Type (EIT) for Serafin title, variable names and units
SLF_EIT = 'iso-8859-1'


VARIABLES_ID_2D, VARIABLES_ID_3D = {'fr': {}, 'en': {}}, {'fr': {}, 'en': {}}


def build_variables_table():
    base_folder = os.path.dirname(os.path.realpath(__file__))
    for dic, name in zip([VARIABLES_ID_2D, VARIABLES_ID_3D], ['Serafin_var2D.csv', 'Serafin_var3D.csv']):
        with open(os.path.join(base_folder, 'data', name), 'r') as f:
            f.readline()  # header
            for line in f.readlines():
                var_id, var_name_fr, var_name_en, _ = line.rstrip().split(';')
                dic['fr'][var_name_fr] = var_id
                dic['en'][var_name_en] = var_id


build_variables_table()


class SerafinValidationError(Exception):
    """!
    @brief Custom exception for Serafin file content check
    """
    def __init__(self, message):
        """!
        @param message <str>: error message description
        """
        super().__init__(message)
        self.message = message
        logger.error('SERAFIN VALIDATION ERROR: %s' % message)


class SerafinRequestError(Exception):
    """!
    @brief Custom exception for requesting invalid values from Serafin object
    """
    def __init__(self, message):
        """!
        @param message <str>: error message description
        """
        super().__init__(message)
        self.message = message
        logger.error('SERAFIN REQUEST ERROR: %s' % message)


class SerafinHeader:
    """!
    @brief: Data type for reading and storing the Serafin file header

    # Attributes:
    ## Sizes
    - file_size <int>: total file size
    - header_size <int>: size taken by header only (set by `_set_header_size`)
    - frame_size <int>: size taken by a single frame (set by `_set_frame_size`)

    ## Float precision: simple or double precision
        (attributes are set by `_set_as_single_precision` or `_set_as_double_precision`)
    - float_type <str>: 'f' or 'd'
    - float_size <int>: 4 or 8
    - np_float_type: np.float32 or np.float64

    - endian <str>: file endianness ('>' = big-endian, '<' = little-endian)

    - title <bytes:72>: title of the simulation
    - file_format <bytes:8>: file format type (e.g. b'SERAFIN ')
    - language <str>: language for variables ('fr' or 'en')

    - is_2d <bool>: True in 2D else False
    - has_knolg <bool>: True if ipobo is replaced by KNOLG array
    - date <[int]>: list with 6 integers (year, month, day, hour, minute and second) or None if not available
    - nb_frames <int>: number of frames

    - nb_var <int>: number of variables
    - nb_var_quadratic <int>: ?
    - nb_nodes_per_elem <int>: number of nodes per element
    - nb_planes <int>: number of layers (should be 0 in 2D)

    - var_IDs <[str]>: variable identifiers
    - var_names <[str]>: variable names
    - var_units <[str]>: variable units

    - params <(int)>: tuple of 10 integer parameters
    - nb_elements <int>: number of 3D elements
    - nb_nodes <int>: number of 3D nodes
    - nb_nodes_per_elem <int>: number of nodes per element (= 3 in 2D and 6 in 3D)
    - nb_nodes_2d <int>: number of 2D nodes (equals to `nb_nodes` in 2D)

    - mesh_origin <(float, float)>: x and y shift to apply to written coordinates (set by `set_mesh_origin`)
    - x_stored <numpy.1D-array>: east written coordinates [shape = nb_nodes]
    - y_stored <numpy.1D-array>: north written coordinates [shape = nb_nodes]
    - x <numpy.1D-array>: east coordinates [shape = nb_nodes] (set by `_compute_mesh_coordinates`)
    - y <numpy.1D-array>: north coordinates [shape = nb_nodes] (set by `_compute_mesh_coordinates`)
    - ikle <numpy.1D-array>: connectivity table with 1-indexed nodes number [shape = nb_nodes_per_elem * nb_elements]
    - ikle_2d <numpy.2D-array>: reshaped connectivity table
        [shape = (nb_elements, nb_nodes_per_elem)] (set by `_build_ikle_2d`)
    - ipobo <numpy.1D-array>: array with 0 values for inner nodes and 1-indexed node number for boundary nodes
        [shape = nb_nodes]
    """
    def __init__(self, title='', format_type='SERAFIN ', lang=settings.LANG, endian='>'):
        """
        @param title <str>: title of the simulation
        @param format_type <str>:
        @param lang <str>: language for variables
        """
        self.file_size = -1
        self.header_size = -1
        self.frame_size = -1

        self.float_type = ''
        self.float_size = -1
        self.np_float_type = None

        self.endian = endian

        self.title = bytes(title, SLF_EIT).ljust(72)
        self.file_format = b''.ljust(8)
        self._set_file_format_and_precision(format_type)

        if lang not in ('fr', 'en'):
            raise SerafinRequestError('Language (for Serafin variables) %s is not implemented' % lang)
        self.language = lang

        self.is_2d = True
        self.has_knolg = False
        self.date = None

        self.nb_var = 0
        self.nb_var_quadratic = 0
        self.nb_planes = 0
        self.nb_frames = 0

        self.var_IDs = []
        self.var_names = []
        self.var_units = []

        self.params = (1, 0, 0, 0, 0, 0, 0, 0, 0, 0)
        self.nb_elements = -1
        self.nb_nodes = -1
        self.nb_nodes_per_elem = -1
        self.nb_nodes_2d = -1

        self.mesh_origin = (0, 0)
        self.x_stored = None
        self.y_stored = None
        self.x = None
        self.y = None
        self.ikle = None
        self.ikle_2d = None
        self.ipobo = None

    @property
    def np_type(self):
        return np.dtype(self.np_float_type).newbyteorder(self.endian)

    def _check_dim(self):
        # verify data consistence and determine 2D or 3D
        if self.is_2d:
            if self.nb_nodes_per_elem != 3:
                raise SerafinValidationError('Unknown mesh type')
        else:
            if self.nb_nodes_per_elem != 6:
                raise SerafinValidationError('The number of nodes per element is not equal to 6')
            if self.nb_planes < 2:
                raise SerafinValidationError('The number of planes is less than 2')

    def _set_file_format_and_precision(self, file_format):
        """!
        @brief: Set some attributes to read/write single or double precision Serafin depending on file format
        @file_format <str>: Serafin file format (max length is 8)
        If file format is not recognized, the file is expected to be simple precision
        """
        self.file_format = bytes(file_format, SLF_EIT).ljust(8)
        if file_format in ('SERAFIND', 'SELAFIND', '       D'):
            self._set_as_double_precision()
        else:
            if file_format not in ('SERAFIN ', 'SERAFINS', 'SELAFIN ', 'SERAPHIN'):
                logger.warning('Format "%s" is unknown and is forced to "SERAFIN "' % file_format)
                self.file_format = bytes('SERAFIN', SLF_EIT).ljust(8)
            self._set_as_single_precision()

    def _set_has_knolg(self):
        self.has_knolg = (self.params[7] != 0 or self.params[8] != 0)

    def build_params(self):
        self.params = (
            1,
            0,
            self.mesh_origin[0],
            self.mesh_origin[1],
            0,
            0,
            self.nb_planes,
            0,
            0,
            0 if self.date is None else 1
        )

    def _build_ikle_2d(self):
        if self.is_2d:
            self.ikle_2d = self.ikle.reshape(self.nb_elements, self.nb_nodes_per_elem)
        else:
            ikle = self.ikle.reshape(self.nb_elements, self.nb_nodes_per_elem)
            self.ikle_2d = np.empty([self.nb_elements // (self.nb_planes - 1), 3], dtype=np.int64)
            nb_lines = self.ikle_2d.shape[0]
            # test the integer division
            if nb_lines * (self.nb_planes - 1) != self.nb_elements:
                raise SerafinValidationError('The number of elements is not divisible by (number of planes - 1)')
            for i in range(nb_lines):
                self.ikle_2d[i] = ikle[i, [0, 1, 2]]

    def _set_as_single_precision(self):
        """Set Serafin as single precision"""
        self.float_type = 'f'
        self.float_size = 4
        self.np_float_type = np.float32

    def _set_as_double_precision(self):
        """Set Serafin as double precision"""
        self.float_type = 'd'
        self.float_size = 8
        self.np_float_type = np.float64

    def unpack_int(self, bytes2unpack, nb=1):
        """
        Unpack bytes to integer(s)
        @param bytes2unpack <bytes>: bytes to unpack
        @param nb <int>: number of consecutive integers
        @return <(int)>
        """
        fmt = self.endian + str(nb) + 'i'
        return struct.unpack(fmt, bytes2unpack)

    def unpack_float(self, bytes2unpack, nb=1):
        """
        Unpack bytes to float(s)
        @param bytes2unpack <bytes>: bytes to unpack
        @param nb <int>: number of consecutive float
        @return <(float)>
        """
        fmt = self.endian + str(nb) + self.float_type
        return struct.unpack(fmt, bytes2unpack)

    def pack_int(self, *args, nb=1):
        """
        Pack integers
        @param args <(int)>: integers to pack
        @param nb <int>: number of integer values
        @return <bytes>
        """
        fmt = self.endian + str(nb) + 'i'
        return struct.pack(fmt, *args)

    def pack_float(self, *args, nb=1):
        """
        Pack floats
        @param args <(float)>: floats to pack
        @param nb <int>: number of float values
        @return <bytes>
        """
        fmt = self.endian + str(nb) + self.float_type
        return struct.pack(fmt, *args)

    def toggle_endianness(self):
        """Toggle original endianness (between big or little endian)"""
        if self.endian == '>':
            self.endian = '<'
        else:
            self.endian = '>'
        logger.debug('Toggle endianness to %s' % ('big' if self.endian == '>' else 'litte'))

    def _compute_mesh_coordinates(self):
        """Compute mesh coordinates from origin"""
        if settings.ENABLE_MESH_ORIGIN:
            self.x = self.mesh_origin[0] + self.x_stored
            self.y = self.mesh_origin[1] + self.y_stored
        else:
            self.x = self.x_stored
            self.y = self.y_stored

    def _set_header_size(self):
        """Set header size"""
        nb_ikle_values = self.nb_elements * self.nb_nodes_per_elem
        coord_size = self.nb_nodes * self.float_size
        self.header_size = (80 + 8) + (8 + 8) + (self.nb_var * (8 + 32)) \
                                    + (40 + 8) + (self.params[-1] * ((6 * 4) + 8)) + (16 + 8) \
                                    + (nb_ikle_values * 4 + 8) + (self.nb_nodes * 4 + 8) + 2 * (coord_size + 8)

    def _set_frame_size(self):
        """Set frame size (all variable values for one time step)"""
        self.frame_size = 8 + self.float_size + (self.nb_var * (8 + self.nb_nodes * self.float_size))

    def _expected_file_size(self):
        """Returns expected file size"""
        return self.header_size + self.nb_frames * self.frame_size

    def summary(self):
        template = 'The file is of type {} {}. It has {} variable{}{},\n' \
                   'on {} nodes and {} elements for {} time frame{}.'
        return template.format(self.file_format.decode(SLF_EIT),
                               {True: '2D', False: '3D'}[self.is_2d], self.nb_var,
                               ['', 's'][self.nb_var > 1], '' if self.is_2d else ', %d layers' % self.nb_planes,
                               self.nb_nodes, self.nb_elements, self.nb_frames,
                               ['', 's'][self.nb_frames > 1])

    def copy(self):
        """Returns a deep copy of the current instance"""
        return copy.deepcopy(self)

    def copy_as_2d(self):
        """!
        Returns a 2D equivalent copy of the current instance
        @return <slf.Serafin.SerafinHeader>: output Serafin header
        """
        if self.is_2d:
            raise SerafinRequestError('Cannot convert header to a 2D equivalent because the input is not 3D')

        ori_params = self.params
        nb_planes = self.nb_planes
        new_header = self.copy()

        # Overwrites relevant attributes
        new_header.nb_planes = 0
        new_params = list(ori_params)
        new_params[6] = new_header.nb_planes
        new_header.params = tuple(new_params)
        new_header.is_2d = True
        new_header.nb_elements //= (nb_planes - 1)
        new_header.nb_nodes //= nb_planes
        new_header.nb_nodes_per_elem = 3
        new_header.nb_nodes_2d = new_header.nb_nodes
        npd = new_header.nb_nodes_per_elem
        new_header.ikle = np.take(self.ikle, [2*npd*i+j for i in range(new_header.nb_elements) for j in range(3)])
        new_header.ipobo = self.ipobo[:self.nb_nodes_2d]
        new_header.x_stored = self.x_stored[:self.nb_nodes_2d]
        new_header.y_stored = self.y_stored[:self.nb_nodes_2d]
        new_header._compute_mesh_coordinates()

        # Update sizes
        new_header._set_header_size()
        new_header._set_frame_size()
        new_header.file_size = new_header._expected_file_size()

        return new_header

    def copy_as_3d(self, nb_planes):
        """!
        Returns a 3D equivalent copy of the current instance
        @param nb_planes <int>: number of planes
        @return <slf.Serafin.SerafinHeader>: output Serafin header
        """
        if not self.is_2d:
            raise SerafinRequestError('Cannot convert header to a 3D equivalent because the input is not 2D')
        if nb_planes < 2:
            raise SerafinRequestError('A 3D file has to contain at least 2 planes')
        ori_params = self.params
        new_header = self.copy()

        # Overwrites relevant attributes
        new_header.nb_planes = nb_planes
        new_params = list(ori_params)
        new_params[6] = new_header.nb_planes
        new_header.params = tuple(new_params)
        new_header.is_2d = False
        new_header.nb_elements *= (nb_planes - 1)
        new_header.nb_nodes *= nb_planes
        new_header.nb_nodes_per_elem = 6

        ikle_bottom_pattern = np.concatenate((self.ikle_2d, self.ikle_2d + new_header.nb_nodes_2d), axis=1)
        ikle = np.empty((nb_planes - 1, self.nb_elements, new_header.nb_nodes_per_elem), dtype=np.int64)
        for i in range(nb_planes - 1):
            ikle[i] = ikle_bottom_pattern + i * new_header.nb_nodes_2d
        new_header.ikle = ikle.flatten()
        new_header._build_ikle_2d()

        ipobo = np.empty((nb_planes, new_header.nb_nodes_2d), dtype=np.int64)
        for i in range(nb_planes):
            ipobo[i] = self.ipobo + i * self.ipobo.max()
            ipobo[i][self.ipobo == 0] = 0
        new_header.ipobo = ipobo.flatten()

        new_header.x_stored = np.tile(self.x_stored, nb_planes)
        new_header.y_stored = np.tile(self.y_stored, nb_planes)
        new_header._compute_mesh_coordinates()

        # Update sizes
        new_header._set_header_size()
        new_header._set_frame_size()
        new_header.file_size = new_header._expected_file_size()

        return new_header

    def nearest_node(self, target_x, target_y):
        """!
        Find the nearest node of a target point (from x and y coordinates)
        @param target_x <float>: east target coordinate
        @param target_y <float>: north target coordinate
        @return <int>: node number (1-indexed)
        """
        dist = np.sqrt(np.power(self.x - target_x, 2) + np.power(self.y - target_y, 2))
        return np.argmin(dist) + 1

    def same_2d_mesh(self, other):
        """!
        @brief: Check if the other mesh is strictly identical (same order of nodes and elements) on the horizontal
        @param other <SerafinHeader>: header to compare
        @return: bool
        """
        # Speedup in comparing by increasing complexity
        if self.nb_nodes_2d != other.nb_nodes_2d or self.nb_elements != other.nb_elements:
            return False
        elif np.all(self.x_stored != other.x_stored) or np.all(self.y_stored != other.y_stored):
            return False
        elif np.all(self.ikle != other.ikle) or np.all(self.ipobo != other.ipobo):
            return False
        else:
            return True

    def is_double_precision(self):
        return self.float_type == 'd'

    def to_single_precision(self):
        self.file_format = bytes('SERAFIN', SLF_EIT).ljust(8)
        self.float_type = 'f'
        self.float_size = 4
        self.np_float_type = np.float32
        self._set_frame_size()
        self._set_header_size()
        self.file_size = self._expected_file_size()

    def empty_variables(self):
        """Empty all variables"""
        self.nb_var = 0
        self.var_IDs, self.var_names, self.var_units = [], [], []

    def add_variable(self, var_ID, var_name, var_unit):
        """!
        @brief: Add a single variable
        @param var_ID <str>: variables identifier (abbreviation)
        @param var_name <bytes>: variable name
        @param var_unit <bytes>: variable unit
        """
        self.nb_var += 1
        self.var_IDs.append(var_ID)
        self.var_names.append(var_name)
        self.var_units.append(var_unit)

    def add_variable_str(self, var_ID, var_name, var_unit):
        """!
        @brief: Add a single variable with strings
        @param var_ID <str>: variables identifier (abbreviation)
        @param var_name <str>: variable name
        @param var_unit <str>: variable unit
        """
        self.nb_var += 1
        self.var_IDs.append(var_ID)
        self.var_names.append(bytes(var_name, SLF_EIT).ljust(16))
        self.var_units.append(bytes(var_unit, SLF_EIT).ljust(16))

    def add_variable_from_ID(self, var_ID):
        """!
        @brief: Add new variable from its ID
        @param var_ID <str>: variable ID
        """
        try:
            if self.is_2d:
                var_name = VARIABLES_2D[var_ID].name(self.language)
                var_unit = VARIABLES_2D[var_ID].unit()
            else:
                var_name = VARIABLES_3D[var_ID].name(self.language)
                var_unit = VARIABLES_3D[var_ID].unit()
        except KeyError:
            raise SerafinRequestError('The variable "%s" is not known (lang=%s)' % (var_ID, self.language))
        self.add_variable_str(var_ID, var_name, var_unit)

    def set_mesh_origin(self, x, y):
        """!
        @brief: Set mesh origin coordinates (/!\ coordinates should be integers!)
        @param x <int>: X-coordinate of the origin
        @param y <int>: Y-coordinate of the origin
        """
        assert isinstance(x, int) and isinstance(y, int)
        self.mesh_origin = (x, y)
        params = list(self.params)
        params[2] = x
        params[3] = y
        self.params = tuple(params)

    def set_variables(self, selected_vars):
        """!
        @brief: Set new variables
        @param selected_vars <[str, bytes, bytes]>: list composed of variable ID, name and unit
        """
        self.empty_variables()
        for var_ID, var_name, var_unit in selected_vars:
            self.add_variable(var_ID, var_name, var_unit)

    def iter_on_all_variables(self):
        """!
        Iterate on variables
        @return <str, bytes, bytes>: variable ID, name and unit
        """
        for var_ID, var_name, var_unit in zip(self.var_IDs, self.var_names, self.var_units):
            yield var_ID, var_name, var_unit

    def transform_mesh_copy(self, transformations):
        """!
        @brief Apply transformations on 2D nodes of a mesh copy
        @param transformations <[geom.transformation.Transformation]>: list of successive transformations
        @return: modified copy of original header with transformed mesh nodes
        """
        if not transformations:
            return self.copy()
        points = [np.array([x, y, 0]) for x, y in zip(self.x, self.y)]
        for t in transformations:
            points = [t(p) for p in points]
        new_header = self.copy()
        new_header.x_stored = np.array([p[0] for p in points])
        new_header.y_stored = np.array([p[1] for p in points])
        self.set_mesh_origin(0, 0)
        self._compute_mesh_coordinates()
        return new_header

    def transform_mesh(self, transformations):
        """!
        @brief Apply transformations on mesh nodes (only in 2D)
        @param transformations <[geom.transformation.Transformation]>: list of successive transformations
        """
        if not transformations:
            return
        points = [np.array([x, y, 0]) for x, y in zip(self.x, self.y)]
        for t in transformations:
            points = [t(p) for p in points]
        self.x_stored = np.array([p[0] for p in points])
        self.y_stored = np.array([p[1] for p in points])
        self.set_mesh_origin(0, 0)
        self._compute_mesh_coordinates()

    def get_all_edges(self):
        """Get all edges (pair of nodes)"""
        edges = np.zeros((3 * len(self.ikle_2d), 2), dtype=np.int64)
        for i, (n1, n2, n3) in enumerate(self.ikle_2d):
            edges[3 * i, :] = [n1, n2]
            edges[3 * i + 1, :] = [n2, n3]
            edges[3 * i + 2, :] = [n3, n1]
        return edges

    def get_external_edges(self):
        """Get external edges (pair of nodes)"""
        edges = self.get_all_edges()
        # Trick to identify unique pair of nodes (even if node orders might differ) in defining a strange function
        edges_multi = edges[:, 0] * edges[:, 1] / (edges[:, 0] + edges[:, 1])
        unique, unique_inverse, unique_counts = np.unique(edges_multi, return_inverse=True, return_counts=True)
        # A boundary node is connected only once to another node (not twice!)
        boundary_edges = edges[unique_counts[unique_inverse] == 1]
        return boundary_edges

    def iter_on_boundaries(self):
        """
        Iterate over all boundaries to get the nodes describing them
        Each element is an ordered list of nodes (1-indexed numbering)

        How boundaries are defined:
        - the first boundary is the external boundary and then the islands (internal boundaries) are described
            in an arbitrary order
        - the external boundary is described counter-clockwise
        - the islands are described clockwise
        - the first boundary node should be the node with the minimum value of x+y (corresponds to the bottom left corner)
        """
        boundary_edges = self.get_external_edges()

        # Build boundaries by iteration on all boundary edges (for each boundary, from first node until it loops)
        id_boundary = 1
        while len(boundary_edges) != 0:
            boundary_nodes = np.unique(boundary_edges.flatten())  # Node numbering 1-indexed
            x_plus_y = self.x[boundary_nodes - 1] + self.y[boundary_nodes - 1]

            # current_boundary_nodes, first_node, prev_node and next_node contain 1-indexed node(s)
            first_node = boundary_nodes[np.argmin(x_plus_y)]
            logger.debug("Build new boundary from node %i among %i nodes" % (first_node, len(boundary_nodes)))
            prev_node = copy.deepcopy(first_node)
            next_node = -1

            # Build list of nodes describing the boundary (/!\ first and last node are explicitly duplicated):
            current_boundary_nodes = [first_node]
            while next_node != first_node:
                try:
                    index = np.where(boundary_edges == prev_node)[0][0]
                except IndexError:
                    logger.critical(np.where(boundary_edges == prev_node))
                    raise SerafinRequestError('Unexpected error while determining next boundary node after node %i'
                                              % prev_node)
                n1, n2 = boundary_edges[index, :]
                boundary_edges = np.delete(boundary_edges, index, axis=0)
                next_node = n1 if n2 == prev_node else n2
                prev_node = next_node
                current_boundary_nodes.append(next_node)

            # Determine if boundary is clock-wise
            if len(current_boundary_nodes) > 2:
                boundary_geom = LinearRing([(self.x[n - 1], self.y[n - 1]) for n in current_boundary_nodes[:-1]])
                ccw = boundary_geom.is_ccw
            else:
                ccw = True  # arbitrary value (order can not be defined!)

            # Reverse node ordering (if necessary) and remove last duplicated node
            if id_boundary == 1:  # this is the first boundary (external)
                if not ccw:
                    current_boundary_nodes.reverse()
            else:  # current boundary is an island
                if ccw:
                    current_boundary_nodes.reverse()
            current_boundary_nodes.pop()
            logger.debug("Boundary %i has %i nodes" % (id_boundary, len(current_boundary_nodes)))
            yield current_boundary_nodes
            id_boundary += 1

    def build_ipobo(self):
        """
        Build IPOBO array containing 0 values for inner nodes and 1-indexed node number for boundary nodes
        Beware: This method will probably crash if some nodes are duplicated!
        """
        ipobo_2d = np.zeros(self.nb_nodes_2d, dtype=np.int64)

        try:
            id_boundary_node = 0
            for boundary_nodes in self.iter_on_boundaries():
                for n in boundary_nodes:
                    id_boundary_node += 1
                    ipobo_2d[n - 1] = id_boundary_node

            self.ipobo = ipobo_2d
            if not self.is_2d:
                shift_ipobo = np.zeros(self.nb_nodes_2d)
                shift_ipobo[ipobo_2d > 0] = id_boundary_node
                for i_plan in range(self.nb_planes):
                    if i_plan > 0:
                        self.ipobo = np.concatenate((self.ipobo, ipobo_2d + i_plan * shift_ipobo))
        except SerafinRequestError:
            logger.warning("The IPOBO table could not be built and set to 0. Check if some nodes are superimposed.")
            self.ipobo = np.zeros(self.nb_nodes, dtype=np.int64)

    def _set_as_2d(self):
        """!
        Beware: nb_nodes_2d has to be consistant
        """
        self.is_2d = True
        self.nb_nodes_2d = self.nb_nodes
        self.nb_planes = 0
        self.nb_nodes_per_elem = 3

    def from_triangulation(self, nodes, ikle, ipobo=None):
        """!
        Set to Serafin 2D header from a given triangulation

        @param nodes <numpy 2D-array>: x and y coordinates
        @param ikle <numpy 2D-array>: connectivity table (1-indexed)
        @param ipobo <numpy 1D-array>: boundary indicator table
        """
        assert ikle.min() == 1 and ikle.max() == len(nodes)  # check arrays are 1-indexed
        self.nb_nodes = nodes.shape[0]
        self._set_as_2d()
        self.nb_elements = ikle.shape[0]
        self.x_stored = nodes[:, 0]
        self.y_stored = nodes[:, 1]
        self._compute_mesh_coordinates()
        self.ikle = ikle.flatten()
        self._build_ikle_2d()
        self.build_params()
        if ipobo is None:
            self.build_ipobo()
        else:
            if ipobo.shape != (len(nodes),):
                raise SerafinValidationError("IPOBO table is not a 1D-array with length of %i." % len(nodes))
            self.ipobo = ipobo

    def from_file(self, file, file_size):
        """!
        @param file <_io.BufferedReader>: input Serafin stream
        @param file_size <int>: file size (in bytes)
        @return <slf.Serafin.SerafinHeader>: output Serafin header
        """
        # Check if file is empty (usefull if re-runs after a crash)
        if self.file_size == 0:
            raise SerafinValidationError('File is empty (file size is equal to 0)')
        self.file_size = file_size

        # Determine binary file endianness from first integer
        first_int_block = file.read(4)
        if struct.unpack('>i', first_int_block)[0] == 80:
            self.endian = '>'
        elif struct.unpack('<i', first_int_block)[0] == 80:
            self.endian = '<'
        else:
            raise SerafinValidationError('File endianness could not be determined')
        logger.debug('File is determined to be %s endian' % ('big' if self.endian == '>' else 'litte'))

        # Read title
        self.title = file.read(72)
        file_format = file.read(8)
        file.read(4)

        try:
            data_format = file_format.decode(SLF_EIT)
            logger.debug('The file type is: "%s"' % data_format)
        except UnicodeDecodeError:
            raise SerafinValidationError('File type is unreadable: %s' % file_format)
        self._set_file_format_and_precision(data_format)

        # Read the number of linear and quadratic variables
        file.read(4)
        self.nb_var = self.unpack_int(file.read(4), 1)[0]
        self.nb_var_quadratic = self.unpack_int(file.read(4), 1)[0]
        logger.debug('The file has %d variables' % self.nb_var)
        file.read(4)
        if self.nb_var_quadratic != 0:
            raise SerafinValidationError('The number of quadratic variables is not equal to zero')

        # Read variable names and units
        for _ in range(self.nb_var):
            file.read(4)
            self.var_names.append(file.read(16))
            self.var_units.append(file.read(16))
            file.read(4)

        # IPARAM: 10 integers (not all are useful...)
        file.read(4)
        self.params = self.unpack_int(file.read(40), 10)
        file.read(4)
        self.mesh_origin = self.params[2], self.params[3]
        self.nb_planes = self.params[6]

        self.is_2d = (self.nb_planes == 0)

        if self.params[-1] == 1:
            # Read 6 integers which correspond to simulation starting date
            file.read(4)
            self.date = self.unpack_int(file.read(6 * 4), 6)
            file.read(4)
        else:
            self.date = None

        self._set_has_knolg()

        # 4 very important integers
        file.read(4)
        self.nb_elements = self.unpack_int(file.read(4), 1)[0]
        self.nb_nodes = self.unpack_int(file.read(4), 1)[0]
        self.nb_nodes_per_elem = self.unpack_int(file.read(4), 1)[0]
        test_value = self.unpack_int(file.read(4), 1)[0]
        if test_value != 1:
            raise SerafinValidationError('The magic number is not equal to one')
        file.read(4)

        self._check_dim()
        logger.debug('The file is determined to be %s' % {True: '2D', False: '3D'}[self.is_2d])

        # determine the number of nodes in 2D
        if self.is_2d:
            self.nb_nodes_2d = self.nb_nodes
        else:
            self.nb_nodes_2d = self.nb_nodes // self.nb_planes

        # IKLE
        file.read(4)
        nb_ikle_values = self.nb_elements * self.nb_nodes_per_elem
        self.ikle = np.frombuffer(file.read(4 * nb_ikle_values),
                                  dtype=np.dtype(np.int32).newbyteorder(self.endian))
        file.read(4)

        # IPOBO
        file.read(4)
        self.ipobo = np.frombuffer(file.read(4 * self.nb_nodes),
                                   dtype=np.dtype(np.int32).newbyteorder(self.endian))
        # A valid IPOBO should not be equal to zero array
        if not np.any(self.ipobo):
            logger.warning('The IPOBO array seems corrupted (zeros array). Try to rebuild it with `build_ipobo()`.')
        file.read(4)

        # x coordinates
        file.read(4)
        coord_size = self.nb_nodes * self.float_size
        self.x_stored = np.frombuffer(file.read(coord_size), dtype=self.np_type)
        file.read(4)

        # y coordinates
        file.read(4)
        self.y_stored = np.frombuffer(file.read(coord_size), dtype=self.np_type)
        file.read(4)

        self._compute_mesh_coordinates()

        # Compute and set header and frame sizes
        self._set_header_size()
        self._set_frame_size()

        # Deduce the number of frames and test the integer division
        self.nb_frames = (self.file_size - self.header_size) // self.frame_size
        logger.debug('The file has %d frames of size %d bytes' % (self.nb_frames, self.frame_size))

        diff_size = self.file_size - self.header_size - self.frame_size * self.nb_frames
        # A difference of only one byte is tolerated.
        # Indeed some old files may contain an ending \x0A character (Linux line feed)
        if diff_size != 0 and diff_size != 1:
            raise SerafinValidationError('Something wrong with the file size (header and frames). '
                                         'File is probably corrupted, difference of %i bytes' % diff_size)

        # Deduce variable IDs from names
        var_table = VARIABLES_ID_2D[self.language] if self.is_2d else VARIABLES_ID_3D[self.language]
        for var_name in self.var_names:
            name = var_name.decode(encoding=SLF_EIT).strip()
            if name not in var_table:
                slf_type = '2D' if self.is_2d else '3D'
                logger.warning('The %s variable name "%s" is not known (lang=%s). '
                               'The complete name will be used as ID' % (slf_type, name, self.language))
                var_id = name
            else:
                var_id = var_table[name]
            self.var_IDs.append(var_id)

        self._build_ikle_2d()

        logger.debug('Finished reading the header')
        return self


class Serafin:
    """!
    @brief A Serafin object corresponds to a single Serafin in file IO stream

    # Attributes:
    - language <str>: language for variables ('fr' or 'en')
    - mode <str>: file open mode
    - file <_io.BufferedReader>: input Serafin stream
    - filename <str>: path to file
    - file_size <int>: size of file
    """
    def __init__(self, filename, mode, language):
        self.language = language
        self.mode = mode

        self.file = None  # will be opened when called using `with` statement
        self.filename = filename
        self.file_size = None

    def __enter__(self):
        self.file = open(self.filename, self.mode)
        return self

    def __exit__(self, exc_type, exc_val, exc_tb):
        self.file.close()
        return False


class Read(Serafin):
    """!
    @brief Serafin file input stream

    # Additional attributes:
    - header <SerafinHeader>: Serafin header
    - time <[float]>: time series in seconds
    """
    def __init__(self, filename, language):
        """!
        @param filename <str>: path to input Serafin file
        @param language <str>: Serafin variable name language ('fr' or 'en')
        """
        super().__init__(filename, 'rb', language)
        self.header = None
        self.time = []
        self.file_size = os.path.getsize(self.filename)
        logger.info('Reading the input file: "%s" of size %d bytes' % (filename, self.file_size))

    def unpack_array(self, size, np_type):
        """!
        @brief Interpret the buffer file as a 1-dimensional array
        @param size <int>: size (number of values * number of bytes)
        @param np_type <np.dtypes.Float32DType>: numpy type format (`>f4` for example)
        """
        return np.frombuffer(self.file.read(size), dtype=np_type)

    def read_header(self):
        """!
        @brief Read the file header and check the file consistency
        """
        self.header = SerafinHeader(lang=self.language)
        self.header.from_file(self.file, self.file_size)

    def get_time(self):
        """!
        @brief Read the time in the Serafin file
        """
        if self.header is None:
            raise SerafinRequestError('Cannot read time without any header (forgot read_header ?)')
        logger.debug('Reading the time series from the file')
        self.file.seek(self.header.header_size, 0)
        for _ in range(self.header.nb_frames):
            self.file.read(4)
            self.time.append(self.header.unpack_float(self.file.read(self.header.float_size), 1)[0])
            self.file.read(4)
            self.file.seek(self.header.frame_size - 8 - self.header.float_size, 1)

    def subset_time(self, start, end, ech):
        """!
        @brief Get a subset of the time frames list
        @param start <float>: starting time (in seconds)
        @param end <float>: ending time (in seconds)
        @param ech <int>: sampling frequency
        @return <[float]>: sampled time serie
        """
        new_time = []
        for time_index, time in enumerate(self.time):
            if start <= time <= end:
                if time_index % ech == 0:
                    new_time.append((time_index, time))
        return new_time

    def _get_var_index(self, var_ID):
        """!
        @brief Handle data request by variable ID
        @param var_ID <str>: the ID of the requested variable
        @return index <int> the index of the frame (0-based)
        """
        if self.header is None:
            raise SerafinRequestError('Cannot extract variable from empty list (forgot read_header ?)')
        try:
            index = self.header.var_IDs.index(var_ID)
        except ValueError:
            raise SerafinRequestError('Variable ID %s not found' % var_ID)
        return index

    def _seek_to_frame(self, time_index, pos_var=0):
        return self.file.seek(
            self.header.header_size + time_index * self.header.frame_size + 8 +
            self.header.float_size + pos_var * (8 + self.header.float_size * self.header.nb_nodes), 0
        )

    def read_var_in_frame(self, time_index, var_ID):
        """!
        @brief Read a single variable in a frame
        @param time_index <int>: the index of the frame (0-based)
        @param var_ID <str>: variable ID
        @return <numpy 1D-array>: values of the variables, of length equal to the number of nodes
        """
        if time_index < 0:
            raise SerafinRequestError('Impossible to read a negative time index!')
        logger.debug('Reading variable %s at frame %i' % (var_ID, time_index))
        pos_var = self._get_var_index(var_ID)
        self._seek_to_frame(time_index, pos_var)
        self.file.read(4)
        return self.unpack_array(self.header.float_size * self.header.nb_nodes, self.header.np_type)

    def read_vars_in_frame(self, time_index, var_IDs=None):
        """!
        @brief Read multiple variables in a frame
        @param time_index <int>: the index of the frame (0-based)
        @param var_IDs <[str]>: list of variable IDs (if not present, all variables are considered)
        @return <numpy 2D-array>: values of the variables with shape (number of variables, number of 2D nodes)
        """
        if var_IDs is None:
            var_IDs = self.header.var_IDs
        if time_index < 0:
            raise SerafinRequestError('Impossible to read a negative time index!')
        logger.debug('Reading variables %s at frame %i' % (var_IDs, time_index))

        res = np.empty((len(var_IDs), self.header.nb_nodes), dtype=self.header.np_float_type)
        for i, var_ID in enumerate(var_IDs):
            pos_var = self._get_var_index(var_ID)
            self._seek_to_frame(time_index, pos_var)
            self.file.read(4)
            res[i, :] = self.unpack_array(self.header.float_size * self.header.nb_nodes, self.header.np_type)
        return res

    def iter_on_all_frames(self):
        """!
        @brief iterate over all frames with time and values
        @return <(float, numpy 2D-array)>: tuple with time and values of the variables with shape
            (number of variables, number of 2D nodes)
        """
        self.file.seek(self.header.header_size, 0)

        res = np.empty((self.header.nb_var, self.header.nb_nodes), dtype=self.header.np_float_type)
        for time_index in range(self.header.nb_frames):
            self.file.read(4)
            time = self.header.unpack_float(self.file.read(self.header.float_size), 1)[0]
            self.file.read(4)

            for i in range(self.header.nb_var):
                self.file.read(4)
                res[i, :] = self.unpack_array(self.header.float_size * self.header.nb_nodes, self.header.np_type)
                self.file.read(4)

            yield time, res

    def read_var_in_frame_as_3d(self, time_index, var_ID):
        """!
        @brief Read a single variable in a 3D frame
        @param time_index <int>: the index of the frame (0-based)
        @param var_ID <str>: variable ID
        @return <numpy 2D-array>: values of the variables with shape (planes number, number of 2D nodes)
        """
        if self.header.is_2d:
            raise SerafinRequestError('Reading values as 3D is only possible in 3D!')
        new_shape = (self.header.nb_planes, self.header.nb_nodes_2d)
        return self.read_var_in_frame(time_index, var_ID).reshape(new_shape)

    def read_vars_in_frame_as_3d(self, time_index, var_IDs=None):
        """!
        @brief Read multiple variables in a 3D frame
        @param time_index <int>: the index of the frame (0-based)
        @param var_IDs <[str]>: list of variable IDs (if not present, all variables are considered)
        @return <numpy 3D-array>: values of the variables with shape
            (number of variables, planes number, number of 2D nodes)
        """
        if self.header.is_2d:
            raise SerafinRequestError('Reading values as 3D is only possible in 3D!')
        if var_IDs is None:
            var_IDs = self.header.var_IDs
        new_shape = (len(var_IDs), self.header.nb_planes, self.header.nb_nodes_2d)
        return self.read_vars_in_frame(time_index, var_IDs).reshape(new_shape)

    def read_var_in_frame_at_layer(self, time_index, var_ID, iplan):
        """!
        @brief Read a single variable in a frame at specific layer
        @param time_index <int>: the index of the frame (0-based)
        @param var_ID <str>: variable ID
        @param iplan <int>: 1-based index of layer
        @return <numpy 1D-array>: values of the variables, of length equal to the number of nodes
        """
        if self.header.is_2d:
            raise SerafinRequestError('Extracting values at a specific layer is only possible in 3D!')
        if iplan < 1 or iplan > self.header.nb_planes:
            raise SerafinRequestError('Layer %i is not inside [1, %i]' % (iplan, self.header.nb_planes))
        return self.read_var_in_frame_as_3d(time_index, var_ID)[iplan + 1]


class Write(Serafin):
    """!
    @brief Serafin file output stream

    (No additional attributes)
    """
    def __init__(self, filename, language, overwrite=False):
        """!
        @param filename <str>: path to output Serafin file
        @param language <str>: Serafin variable name language ('fr' or 'en')
        @param overwrite <bool>: overwrite if file already exists
        """
        mode = 'wb' if overwrite else 'xb'
        super().__init__(filename, mode, language)
        logger.info('Writing the output file: "%s"' % filename)

    def __enter__(self):
        try:
            return Serafin.__enter__(self)
        except FileExistsError:
            raise SerafinRequestError('Cannot overwrite existing file')

    def write_header(self, header):
        """!
        @brief Write Serafin header from attributes
        """
        logger.debug('Writing header with %i nodes, %i elements %s and %i variable %s' %
                     (header.nb_nodes, header.nb_elements,
                      '' if header.is_2d else ', %i layers' % header.nb_planes,
                      header.nb_var, ['', 's'][header.nb_var > 1]))

        # Title and file type
        self.file.write(header.pack_int(80))
        self.file.write(header.title)
        self.file.write(header.file_format)
        self.file.write(header.pack_int(80))

        # Number of variables
        self.file.write(header.pack_int(8))
        self.file.write(header.pack_int(header.nb_var))
        self.file.write(header.pack_int(header.nb_var_quadratic))
        self.file.write(header.pack_int(8))

        # Variable names and units
        for j in range(header.nb_var):
            self.file.write(header.pack_int(2 * 16))
            self.file.write(header.var_names[j].ljust(16))
            self.file.write(header.var_units[j].ljust(16))
            self.file.write(header.pack_int(2 * 16))

        # Date
        self.file.write(header.pack_int(10 * 4))
        self.file.write(header.pack_int(*header.params, nb=10))
        self.file.write(header.pack_int(10 * 4))
        if header.params[-1] == 1:
            self.file.write(header.pack_int(6 * 4))
            self.file.write(header.pack_int(*header.date, nb=6))
            self.file.write(header.pack_int(6 * 4))

        # Number of elements, of nodes, of nodes per element and the magic number
        self.file.write(header.pack_int(4 * 4))
        self.file.write(header.pack_int(header.nb_elements))
        self.file.write(header.pack_int(header.nb_nodes))
        self.file.write(header.pack_int(header.nb_nodes_per_elem))
        self.file.write(header.pack_int(1))  # magic number
        self.file.write(header.pack_int(4 * 4))

        # IKLE
        nb_ikle_values = header.nb_elements * header.nb_nodes_per_elem
        self.file.write(header.pack_int(4 * nb_ikle_values))
        self.file.write(np.array(header.ikle, dtype=np.dtype(np.int32).newbyteorder(header.endian)))
        self.file.write(header.pack_int(4 * nb_ikle_values))

        # IPOBO
        self.file.write(header.pack_int(4 * header.nb_nodes))
        self.file.write(np.array(header.ipobo, dtype=np.dtype(np.int32).newbyteorder(header.endian)))
        self.file.write(header.pack_int(4 * header.nb_nodes))

        # X coordinates
        self.file.write(header.pack_int(header.float_size * header.nb_nodes))
        self.file.write(np.array(header.x_stored, dtype=header.np_type))
        self.file.write(header.pack_int(header.float_size * header.nb_nodes))

        # Y coordinates
        self.file.write(header.pack_int(header.float_size * header.nb_nodes))
        self.file.write(np.array(header.y_stored, dtype=header.np_type))
        self.file.write(header.pack_int(header.float_size * header.nb_nodes))

    def write_entire_frame(self, header, time_to_write, values):
        """!
        @brief write all variables/nodes values
        @param header <SerafinHeader>: output header
        @param time_to_write <float>: output time (in seconds)
        @param values <numpy 2D-array>: values to write, of dimension (nb_var, nb_nodes)
        """
        if values.shape != (header.nb_var, header.nb_nodes):
            raise SerafinValidationError("Shape of values %s is not consistant with SerafinHeader (%i, %i)"
                                         % (str(values.shape), header.nb_var, header.nb_nodes))
        self.file.write(header.pack_int(header.float_size))
        self.file.write(header.pack_float(time_to_write))
        self.file.write(header.pack_int(header.float_size))

        for i in range(header.nb_var):
            self.file.write(header.pack_int(header.float_size * header.nb_nodes))
            self.file.write(np.array(values[i, :], dtype=header.np_type))
            self.file.write(header.pack_int(header.float_size * header.nb_nodes))
